Biochemical conversion of DNA to design polymers format

The design polymer concept, invented and patented by P. Lexow (2004) (Ling-Vitae, Norway), is a biochemical conversion method used to simplify and enhance the way in which information is stored in DNA. According to this technique, natural DNA sequences are converted into code units that make up the design polymers. The code units themselves are short (3-16 nucleotides) DNA fragments having one out of two unique sequences that we schematically label ''0'' or ''1''. Note that each unit represents a single bit of information. Thus, to represent the four bases in the DNA molecules, two bits (or two code units) are needed. The specific sequences and length of the two code units can be specified by the user prior to the conversion of the DNA, and are tailored to optimize its detection by the readout method. The biochemical conversion produces design polymer DNA molecules that are made out of a concatenation of the code units. The information is stored in the order in which the code units are concatenated. For example, adenine can be represented by the code units

"00", thymine by "01", guanine by "10", and cytosine by "11". Thus the sequence (in the native DNA) such as "ATGC" may be represented by: "0001 1011''.

The biochemical conversion method can be used in conjunction with the nanoelectrode-gated tunneling method as described above, and with the optical nanopore detection. Not only does it reduce the four letters in the DNA to binary information, but principally it also magnifies their representation to facilitate single molecule detection. To synthesize design polymers, target DNA molecules are sheared to small pieces (less than 1 Kb) and are ligated with DNA adapters that include a recognition site for the restriction enzyme Mmel. This enzyme cuts 20 bp into the unknown DNA sequence, leaving a two base overhang. This overhang is used for ligation with another DNA adapter that contains a recognition site for another restriction enzyme SfaNI. Following this preparation stage, a cyclic conversion that includes three repeating steps starts. In each cycle the DNA is cleaved to expose three new bases in the target DNA and a DNA adapter that includes the coding units corresponding to these three bases is ligated to the other end of the DNA. The selection of only the "correct" DNA adapter is performed by PCR amplification in each cycle. Thus in each cycle three bases are removed from one end of the target DNA, and the six corresponding code units are appended on the other end. Most importantly, this process has been optimized to be highly parallel. Namely, hundreds of different DNA targets can be converted simultaneously in a single test tube (Lexow, 2004).

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